Left panel

The basic elements to perform an analysis are listed on the left panel: select a polarimetry method, a stack to be analyzed and a method of analysis; then click the button ‘Analysis’

select a polarimetry method

The list of methods is available here

Note that when 4POLAR2D or 4POLAR3D is selected, an image registration is required (see here for more details)

download data to be analyzed

`Open file`: select a `.tiff` or `.tif` stack file
`Open folder`: select a folder containing `.tiff` or `.tif` stack files
`Open figure`: select a `.pyfig` pickled file saved from a previous PyPOLAR analysis. For more information on `.pyfig` files, click here

select the method of analysis

Thresholding (manual): thresholding and regions of interest are manually selected for each stack
Thresholding (auto): thresholding and regions of interest are selected for the first stack and applied to each stack to be analyzed in batch mode
Mask (manual): a binary segmentation mask is applied to the analysis; the name of the segmentation mask has to be identical to the one of the stack with a .png extension. The mask file should be in the same folder as the stack.
Mask (auto): batch analysis, similar to Thresholding (auto) but with a segmentation mask applied to each stack. The mask files should be in the same folder as the stacks.

For `Thresholding (auto)` and `Mask (auto)`, the menu icon is changed to

add one or multiple region(s) of interest (ROI)

Click ‘Add ROI’. This selection is made on the Thresholding/Mask tab; for more details on ROIs

For polygon-shaped ROIs, click successively the left mouse button.
For freeform ROIs, click continuously the right mouse button.
Double click to close the ROI.